Extracellular and membrane-associated prostate cancer markers

ABSTRACT

This document relates to methods and materials involved in identifying, assessing, and monitoring prostate cancer in male mammals. For example, this document provides arrays for detecting polypeptides or nucleic acids that can be used to identify prostate cancer in male mammals. In addition, methods and materials for assessing and monitoring prostate cancer in mammals are provided herein.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.12/442,685, filed on Mar. 24, 2009, which is a National Stageapplication under 35 U.S.C. §371 of International Application No.PCT/US2007/079423, having an International Filing Date of Sep. 25, 2007,which claims the benefit of priority to U.S. Provisional PatentApplication Ser. No. 60/847,057, filed on Sep. 25, 2006. The disclosuresof these applications are incorporated herein by reference in theirentirety.

BACKGROUND

1. Technical Field

This document relates to methods and materials involved in identifying,assessing, and monitoring prostate cancer in male mammals.

2. Background Information

Cancer is a general term for diseases characterized by uncontrolled,abnormal growth of cells. The resulting mass, or tumor, can invade anddestroy surrounding normal tissues. In addition, cancer cells from thetumor can spread through the blood or lymph to start new cancers inother parts of the body, or metastases.

Prostate cancer occurs when a malignant tumor forms in the tissue of theprostate. The prostate is a gland in the male reproductive systemlocated below the bladder and in front of the rectum. The main functionof the prostate gland, which is about the size of a walnut, is to makefluid for semen. Although there are several cell types in the prostate,nearly all prostate cancers start in the gland cells. This type ofcancer is known as adenocarcinoma.

Prostate cancer is the second leading cause of cancer-related death inAmerican men. Most of the time, prostate cancer grows slowly. Autopsystudies show that many older men who died of other diseases also hadprostate cancer that neither they nor their doctor were aware of.Sometimes, however, prostate cancer can grow and spread quickly. It isimportant to be able to distinguish prostate cancers that will growslowly from those that will grow quickly since treatment can beespecially effective when the cancer has not spread beyond the region ofthe prostate. Finding ways to detect cancers early can improve survivalrates.

SUMMARY

This document provides methods and materials related to identifying,assessing, and monitoring prostate cancer in male mammals (e.g.,humans). For example, this document provides arrays for detectingpolypeptides or nucleic acids that can be used to identify prostatecancer in mammals. Such arrays can allow prostate cancer to beidentified in mammals based on differences in the levels of manypolypeptides or nucleic acids in biological samples from mammals thathave prostate cancer as compared to the corresponding levels inbiological samples from mammals that do not have prostate cancer.

Screening for prostate cancer has been widely performed by measuringserum levels of prostate-specific antigen (PSA). However, effective useof the PSA serum assay in general population screening is inhibited by alack of sensitivity and specificity. Specific, sensitive, andnon-invasive methods of screening mammals for cancer (e.g., prostatecancer) can allow cancer to be detected earlier. Early detection ofcancer in mammals can allow the mammals to be treated sooner and improvetheir prognosis. Screening methods having adequate specificity with lowfalse positive rates can reduce unnecessary treatment and suffering.

This document is based, in part, on the discovery of nucleic acidsequences that are predicted to encode extracellular ormembrane-associated polypeptides, and that are differentially expressedin cancerous and non-cancerous prostate epithelial cells. This documentalso is based, in part, on the discovery of nucleic acid sequences thatare predicted to encode polypeptides, and that are expressed in prostatecells at a high level relative to other cell types. The levels oftranscripts and/or polypeptides encoded by these nucleic acids can beused to distinguish mammals with prostate cancer from mammals withoutprostate cancer. For example, a mammal that is found to have serumcontaining one or more than one polypeptide encoded by a nucleic acidlisted in Table 2 at a level that is different (e.g., greater than orless than) than the average level observed in control serum can beclassified as having prostate cancer. In some cases, a mammal that isfound to have serum containing one or more than one polypeptide encodedby a nucleic acid listed in Table 2 and one or more than one polypeptideencoded by a nucleic acid listed in Table 3 at a level that is different(e.g., greater than or less than) than the average level observed incontrol serum can be classified as having prostate cancer. In somecases, a mammal that is found to have prostate cells expressing one ormore than one polypeptide encoded by a nucleic acid listed in Table 4 ata level that is greater than the average level observed in controlprostate cells can be classified as having prostate cancer. The levelsof nucleic acids and/or polypeptides encoded by nucleic acids listed inTable 2 also can be used to evaluate cancer aggressiveness, monitorcancer progression, predict cancer outcome, and monitor response totreatment in mammals. In some cases, the level of one or more than onenucleic acid or polypeptide encoded by a nucleic acid listed in Table 2and the level of one or more than one nucleic acid or polypeptideencoded by a nucleic acid listed in Table 3 can be used to evaluatecancer aggressiveness, monitor cancer progression, predict canceroutcome, or monitor the response to cancer treatment in mammals.

In general, one aspect of this document features a method foridentifying a mammal as having prostate cancer. The method comprising,or consists essentially of, (a) determining whether or not a mammal hasa prostate cancer fluid profile, and (b) classifying the mammal ashaving prostate cancer if the mammal has the prostate cancer fluidprofile and classifying the mammal as not having prostate cancer if themammal does not have the prostate cancer fluid profile. The mammal canbe a human. The method can comprise using blood, serum, plasma, urine,semen, or seminal fluid to assess the presence or absence of theprostate cancer fluid profile.

In another aspect, this document features a method for identifying amammal as having prostate cancer. The method comprises, or consistsessentially of, (a) determining whether or not a mammal has a prostatecancer cell profile, and (b) classifying the mammal as having prostatecancer if the mammal has the prostate cancer cell profile andclassifying the mammal as not having prostate cancer if the mammal doesnot have the prostate cancer cell profile. The mammal can be a human.The method can comprise using prostate cells obtained from a needlebiopsy to assess the presence or absence of the prostate cancer cellprofile.

In another aspect, this document features a method for assessing theeffectiveness of a treatment for prostate cancer. The method comprises,of consists essentially of, determining whether or not a mammal havingprostate cancer and having received a treatment for the prostate cancerhas a prostate cancer fluid profile to the same or greater degree thanthat observed prior to the treatment, wherein the presence of theprostate cancer fluid profile to the same or greater degree than thatobserved prior to the treatment indicates that the treatment isineffective. The mammal can be a human. The method can comprise usingblood, serum, plasma, urine, semen, or seminal fluid to assess thepresence or absence of the prostate cancer fluid profile to the same orgreater degree than that observed prior to the treatment.

In another aspect, this document features a method for assessing theeffectiveness of a treatment for prostate cancer. The method comprises,or consists essentially of, determining whether or not a mammal havingprostate cancer and having received a treatment for the prostate cancerhas a prostate cancer cell profile to the same or greater degree thanthat observed prior to the treatment, wherein the presence of theprostate cancer cell profile to the same or greater degree than thatobserved prior to the treatment indicates that the treatment isineffective. The mammal can be a human. The method can comprise usingprostate cells obtained from a needle biopsy to assess the presence orabsence of the prostate cancer cell profile to the same or greaterdegree than that observed prior to the treatment.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other references (e.g.,the records associated with GenBank accession or GI numbers) mentionedherein are incorporated by reference in their entirety. In case ofconflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DETAILED DESCRIPTION

This document provides methods and materials related to identifying,assessing, and monitoring prostate cancer in male mammals. For example,this document provides arrays for detecting nucleic acids orpolypeptides that can be used to identify, assess, and/or monitorprostate cancer in male mammals. Such arrays can allow prostate cancerto be identified, assessed, and/or monitored based on the levels ofnucleic acids or polypeptides in a biological sample from a mammal.

As described herein, this document provides methods and materials foridentifying prostate cancer in male mammals (e.g., humans). In someembodiments, a mammal can be classified as having prostate cancer if itis determined that a biological fluid (e.g., blood, urine, seminalfluid, or serum) from the mammal contains one or more than onepolypeptide (e.g., two, three, four, five, six, seven, eight, nine, 10,15, 20, 25, 30, 35, 40, 45, 50, 55, 60, or more than 60 polypeptides),or a fragment thereof, encoded by a nucleic acid listed in Table 2(e.g., a category 1, 2, or 3 nucleic acid listed in Table 2) at a levelthat is greater than the average level of the same one or more than onepolypeptide observed in corresponding control fluid from controlmammals. In some cases, a mammal can be classified as having prostatecancer if it is determined that a biological fluid (e.g., blood, urine,seminal fluid, or serum) from the mammal contains one or more than onepolypeptide, or fragment thereof, encoded by a nucleic acid listed inTable 2, and one or more than one polypeptide, or fragment thereof,encoded by a nucleic acid listed in Table 3 at a level that is greaterthan the average level of the same one or more than one polypeptideobserved in corresponding control fluid from control mammals. In somecases, a mammal can be classified as having prostate cancer if it isdetermined that prostate cells from the mammal contain one or more thanone nucleic acid or polypeptide, or fragment thereof, encoded by anucleic acid listed in Table 4 (e.g., a category 1, 2, or 3 nucleic acidlisted in Table 4) at a level that is greater than the average level(e.g., via a subset analysis) of the same one or more than one nucleicacid or polypeptide in corresponding control (e.g., non-cancerous)prostate cells.

In some cases, a mammal can be classified as having prostate cancer ifit is determined that a biological fluid (e.g., blood, urine, seminalfluid, or semen) from the mammal has a prostate cancer fluid profile.For the purpose of this document, the term “prostate cancer fluidprofile” as used herein refers to a polypeptide profile in a biologicalfluid (e.g., blood, plasma, serum, urine, semen, or seminal fluid) where16 or more (e.g., 18, 20, 25, 30, 35, 40, 45, 50, 55, 60, or more)polypeptides, or fragments thereof, encoded by nucleic acids listed inTable 2 are present at a level greater than the level observed in acorresponding control biological fluid from a control mammal. In somecases, the prostate cancer fluid profile can be a polypeptide profile ina biological fluid where 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80,85, 90, 95, or 100 percent of the polypeptides, or fragments thereof,encoded by nucleic acids listed in Table 2 are present at a levelgreater than the level observed in corresponding control biologicalfluid from a control mammal.

In some cases, a mammal can be classified as having prostate cancer ifit is determined that prostate cells from the mammal have a prostatecancer cell profile. The term “prostate cancer cell profile” as usedherein refers to a profile where prostate cells express 12 or more(e.g., 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, or more) nucleic acids orpolypeptides, or fragments thereof, encoded by nucleic acids listed inTable 4 at a level greater than the level observed in correspondingcontrol prostate cells. In some cases, the prostate cancer cell profilecan be a profile in prostate cells where 25, 30, 35, 40, 45, 50, 55, 60,65, 70, 75, 80, 85, 90, 95, or 100 percent of the nucleic acids orpolypeptides, or fragments thereof, encoded by nucleic acids listed inTable 4 are present at a level greater than the level observed incorresponding control prostate cells.

Prostate cancer can be identified in any male mammal such as a malehuman, dog, horse, mouse, or rat. The mammal can be middle-aged orolder. For example, a male human can be 35 years old or older (e.g., 40,45, 50, 55, 60, 65, 70, 75 years old or older).

Any biological fluid can be evaluated to determine if it contains one ormore than one polypeptide or nucleic acid, or fragment thereof, encodedby a nucleic acid listed in Table 2 at a level that is greater than theaverage level observed in a corresponding control biological fluid. Forexample, blood (e.g., peripheral blood or venous prostate blood),plasma, serum, urine, semen, and/or seminal fluid can be evaluated todetermine if the fluid contains one or more than one polypeptide ornucleic acid encoded by a nucleic acid listed in Table 2 at a level thatis greater than the average level observed in a corresponding controlbiological fluid. In some cases, a biological fluid (e.g., blood,plasma, serum, urine, semen, and/or seminal fluid) can be evaluated todetermine if the fluid contains one or more than one polypeptide ornucleic acid, or fragment thereof, encoded by a nucleic acid listed inTable 2, and one or more than one polypeptide or nucleic acid, orfragment thereof, encoded by a nucleic acid listed in Table 3 at a levelthat is greater than the average level observed in a correspondingcontrol biological fluid. In some cases, a biological fluid can beevaluated to determine if the fluid has a prostate cancer fluid profile.

Any type of biological sample can be evaluated to determine if itcontains one or more than one nucleic acid or polypeptide, or fragmentthereof, encoded by a nucleic acid listed in Table 4 at a level that isgreater than the average level observed in a corresponding controlbiological sample. For example, biological fluids can be evaluatedincluding, without limitation, blood, plasma, serum, urine, semen, andseminal fluid. In some cases, prostate cells can be evaluated including,without limitation, prostate cells in prostate tissue and metastaticprostate cancer cells in blood, urine, cellular fragments, or in tissuesother than prostate tissue such as lung tissue and lymph node tissue. Insome cases, prostate cells can be evaluated to determine whether or notthe cells have a prostate cancer cell profile.

Any method can be used to obtain a biological sample from a mammal. Forexample, a blood sample can be obtained by peripheral venipuncture, andurine samples can be obtained using standard urine collectiontechniques. In some cases, a tissue sample can be obtained from a tissuebiopsy (e.g., a needle biopsy), from a transurethral resection of theprostate (TURP), or from a radical prostatectomy. A sample can bemanipulated prior to being evaluated for the level of one or more thanone nucleic acid or polypeptide encoded by a nucleic acid listed inTable 2 or 3. A sample also can be manipulated prior to being evaluatedfor a prostate cancer fluid profile or a prostate cancer cell profile.For example, a prostate biopsy specimen can be frozen, embedded, and/orsectioned prior to being evaluated. In addition, nucleic acids and/orpolypeptides can be extracted from a sample, purified, and evaluated todetermine the level of one or more than one nucleic acid or polypeptideencoded by a nucleic acid listed in Table 2 or 3. In some cases, nucleicacids and/or polypeptides extracted from a sample can be evaluated for aprostate cancer cell profile or a prostate cancer fluid profile. In somecases, a tissue sample can be disrupted to obtain a cell lysate. Onceobtained, the cell lysate can be analyzed for the level of one or morethan one polypeptide encoded by a nucleic acid listed in Table 4. A celllysate also can be evaluated for a prostate cancer cell profile. In somecases, prostate cells can be isolated from other cells or tissues priorto analysis. For example, prostate cells can be isolated from tissuesusing laser capture microdissection prior to being evaluated for thelevel of one or more than one nucleic acid or polypeptide encoded by anucleic acid listed in Table 4. In some cases, prostate cells can beevaluated for a prostate cancer cell profile.

The level of any number of nucleic acids or polypeptides encoded bynucleic acids listed in Table 2 can be evaluated to identify prostatecancer. For example, the level of one or more than one (e.g., two,three, four, five, six, seven, eight, nine, 10, 15, 20, 25, 30, 35, 40,45, 50, 55, 60, or more than 60) nucleic acid or polypeptide encoded bya nucleic acid listed in Table 2 can be used to identify prostatecancer. In some cases, the level of one or more than one (e.g., two,three, four, five, six, seven, eight, nine, 10, 15, 20, 25, 30, 35, 40,45, 50, 55, 60, or more than 60) nucleic acid or polypeptide encoded bya nucleic acid listed in Table 2, and the level of one or more than one(e.g., two, three, four, five, six, or more than 6) nucleic acid orpolypeptide encoded by a nucleic acid listed in Table 3 can be used toidentify prostate cancer. In some cases, the level of one or more thanone (e.g., two, three, four, five, six, seven, eight, nine, 10, 15, 20,25, 30, 35, 40, 45, 50, or more than 50) nucleic acid or polypeptideencoded by a nucleic acid listed in Table 4 can be used to identifyprostate cancer.

The level of a nucleic acid or polypeptide encoded by a nucleic acidlisted in Table 2 or 3 in a biological sample can be greater than orless than the average level observed in corresponding control samples.Typically, a nucleic acid or polypeptide can be classified as beingpresent at a level that is greater than or less than the average levelobserved in control samples if the levels differ by at least 10, 20, 30,40, 50, 60, 70, 80, 90, or more percent. In some cases, a nucleic acidor polypeptide can be classified as being present at a level that isgreater than or less than the average level observed in control samplesif the levels differ by greater than 1-fold (e.g., 1.5-fold, 2-fold,3-fold, or more than 3-fold). Control samples typically are obtainedfrom one or more mammals of the same species as the mammal beingevaluated. When identifying prostate cancer, control samples (e.g.,control serum or urine samples) can be obtained from healthy mammals,such as male humans who do not have prostate cancer. In some cases,control samples can be non-cancerous prostate cells or tissues from malemammals having prostate cancer (e.g., non-neoplastic cells adjacent toprostate cancer cells). Control samples can be obtained from any numberof mammals. For example, control samples can be obtained from one ormore mammals (e.g., 10, 20, 30, 40, 50, 75, 100, 200, 300, 400, 500,1000, or more than 1000 mammals) from the same species as the mammalbeing evaluated.

Any method can be used to determine whether or not a polypeptide ispresent in a biological sample at a level that is greater than or lessthan the average level observed in corresponding control samples. Forexample, the level of a particular polypeptide can be measured using,without limitation, immuno-based assays (e.g., ELISA andimmunohistochemistry), Western blotting, arrays for detectingpolypeptides, two-dimensional gel analysis, chromatographic separation,mass spectrometry (MS), tandem mass spectrometry (MS/MS), or liquidchromatography (LC)-MS. Methods of using arrays for detectingpolypeptides include, without limitation, those described herein. Suchmethods can be used to determine simultaneously the relative levels ofmultiple polypeptides.

Any method can be used to determine whether or not a specific nucleicacid is present in a biological samples at a level that is greater thanor less than the average level observed in corresponding controlsamples. For example, the level of a particular nucleic acid can bemeasured using, without limitation, Northern blotting, slot blotting,quantitative PCR, RT-PCR, or chip hybridization techniques. Methods forchip hybridization assays include, without limitation, those describedherein. Such methods can be used to determine simultaneously therelative expression levels of multiple nucleic acids.

Methods provided herein for identifying prostate cancer in male mammalscan be used in combination with one or more methods typically used toidentify prostate cancer. Such methods include, without limitation,digital rectal exam, transrectal ultrasonography, intravenous pyelogram,cystoscopy, and blood and urine tests for levels of prostatic acidphosphatase (PAP) and PSA. A mammal can be evaluated regularly forprostate cancer. For example, a mammal can be evaluated once a year foras long as the mammal is alive. In some cases, male humans can beevaluated for prostate cancer once every year beginning at age 35.Mammals that are susceptible to develop prostate cancer can be screenedmore frequently, and screening can be started at an earlier age. Forexample, mammals having a genetic predisposition to develop cancer, afamily history of cancer, or a trend towards an increased serum level ofone or more polypeptides encoded by a nucleic acid listed in Table 2 canbe assessed more frequently.

This document also provides materials and methods for assessing prostatecancer in a mammal. For example, this document provides materials andmethods for assessing the aggressiveness of prostate cancer in a mammal.Methods typically used to assess the aggressiveness of prostate cancerin a mammal include determining the Gleason score, the serum PSA level,and whether or not the serum PSA level increases over time and rate ofPSA increases (PSA velocity). The Gleason score is a measure of howdifferent cancer cells are from normal cells. The more different thecancer cells are from non-cancer cells, the more likely that the cancerwill spread quickly. In some cases, the aggressiveness of prostatecancer can be assessed based on the numbers and/or levels of nucleicacids or polypeptides encoded by nucleic acids listed in Table 2 in abiological fluid from a mammal. The greater the number of differentnucleic acids or polypeptides encoded by nucleic acids listed in Table 2in a biological fluid from the mammal, the more aggressive the prostatecancer in the mammal. In addition, the greater the differences betweenthe levels of the nucleic acids or polypeptides encoded by nucleic acidslisted in Table 2 in a biological fluid from a mammal and the averagelevels of the same nucleic acids or polypeptides in control samples, themore likely the prostate cancer will move rapidly and progress in themammal. In some embodiments, the aggressiveness of prostate cancer canbe assessed based on the levels of nucleic acids or polypeptides encodedby nucleic acids listed in Table 2, and the level of one or more thanone nucleic acid or polypeptide encoded by a nucleic acid listed inTable 3 in a biological fluid from a mammal. In some cases, the levelsof nucleic acids or polypeptides encoded by nucleic acids listed inTable 2 in a biological fluid can be used in combination with one ormore other factors to determine whether or not a mammal having prostatecancer is susceptible to a poor outcome. For example, levels of nucleicacids or polypeptides encoded by nucleic acids listed in Table 2 in abiological fluid from a mammal having prostate cancer can be used incombination with the clinical stage, the serum PSA level, and/or theGleason pattern of the prostate cancer to determine whether or not themammal is likely to have to a poor outcome. In some cases, theaggressiveness of prostate cancer can be assessed based on the numbersand/or levels of nucleic acids or polypeptides encoded by nucleic acidslisted in Table 4 in a biological sample from a mammal.

Information about the aggressiveness of prostate cancer can be used toguide treatment selection. For example, a mammal identified as havingmore aggressive prostate cancer can be treated earlier and moreaggressively than a mammal identified as having less aggressive prostatecancer. A more aggressive treatment can include radical prostatectomy. Amammal identified as having less aggressive prostate cancer may undergo“watchful waiting” while having little or no standard treatment,particularly if the mammal is elderly.

Once prostate cancer has been identified in a mammal (e.g., a human),the mammal can be subsequently evaluated or monitored over time forprogression of the cancer, particularly if the cancer was identified asbeing aggressive. For example, prostate cancer in a mammal can beassessed as having progressed if it is determined that a biologicalfluid from the mammal (e.g., serum or urine from the mammal) containsone or more than one nucleic acid or polypeptide encoded by a nucleicacid listed in Table 2 at a level that is greater than the level of thesame one or more than one nucleic acid or polypeptide observed in acorresponding biological fluid (e.g., serum or urine) obtainedpreviously from the same mammal. In some cases, prostate cancer in amammal can be assessed as having progressed if it is determined that abiological fluid from the mammal (e.g., serum or urine from the mammal)contains one or more than one nucleic acid or polypeptide encoded by anucleic acid listed in Table 2, and one or more than one nucleic acid orpolypeptide encoded by a nucleic acid listed in Table 3 at a level thatis greater than the level of the same one or more nucleic acids orpolypeptides observed in a corresponding biological fluid (e.g., serumor urine) obtained previously from the same mammal. In some cases,prostate cancer in a mammal can be assessed as having progressed if itis determined that a biological fluid from the mammal has a prostatecancer fluid profile to a level greater than that observed in acorresponding biological fluid obtained previously from the same mammal.In some cases, prostate cancer in a mammal can be assessed as havingprogressed if it is determined that a sample (e.g., a sample of prostatecells) from the mammal contains one or more than one nucleic acid orpolypeptide encoded by a nucleic acid listed in Table 4 at a level thatis greater than the level of the same one or more than nucleic acid orpolypeptide observed in a corresponding sample obtained previously fromthe same mammal. In some cases, prostate cancer in a mammal can beassessed as having progressed if it is determined that a sample (e.g., asample of prostate cells) from the mammal has a prostate cancer cellprofile to a level greater than that observed in a corresponding sampleobtained previously from the same mammal. A mammal can be monitored forprogression of prostate cancer over any period of time with anyfrequency. For example, a male mammal can be monitored once a year,twice a year, three times a year, or more frequently. In some cases, amammal can be monitored every three months for five years or once a yearfor as long as the mammal is alive.

A mammal can also be assessed for progression of prostate cancer before,during, and after treatment for prostate cancer. For example, a mammalcan be assessed for progression (e.g., metastasis) of prostate cancerwhile being treated with androgen deprivation therapy or followingradical prostatectomy. Assessing a mammal for progression of prostatecancer during treatment of the mammal for prostate cancer can allow theeffectiveness of the prostate cancer therapy to be determined. Forexample, a decrease in the level of one or more than one nucleic acid orpolypeptide encoded by a nucleic acid listed in Table 2 in a biologicalfluid (e.g., serum or urine) from a mammal being treated for prostatecancer as compared to the level of the same one or more nucleic acids orpolypeptides observed in a corresponding biological fluid (e.g., serumor urine) obtained previously from the same mammal can indicate that thetherapy is effective. In some cases, a therapy can be assessed as beingeffective if it is determined that a fluid from a mammal having prostatecancer and having received a prostate cancer treatment has a prostatecancer fluid profile to a level less than that observed in correspondingfluid from the same mammal prior to the treatment.

This document also provides methods and materials to assist medical orresearch professionals in determining whether or not a mammal hasprostate cancer. Medical professionals can be, for example, doctors,nurses, medical laboratory technologists, and pharmacists. Researchprofessionals can be, for example, principle investigators, researchtechnicians, postdoctoral trainees, and graduate students. Aprofessional can be assisted by (1) determining the level of one or morethan one polypeptide or nucleic acid encoded by a nucleic acid listed inTable 2 in a sample, and (2) communicating information about that levelto that professional.

Any method can be used to communicate information to another person(e.g., a professional). For example, information can be given directlyor indirectly to a professional. In addition, any type of communicationcan be used to communicate the information. For example, mail, e-mail,telephone, and face-to-face interactions can be used. The informationalso can be communicated to a professional by making that informationelectronically available to the professional. For example, theinformation can be communicated to a professional by placing theinformation on a computer database such that the professional can accessthe information. In addition, the information can be communicated to ahospital, clinic, or research facility serving as an agent for theprofessional.

This document also provides arrays for detecting polypeptides. Thearrays provided herein can be two-dimensional arrays, and can contain atleast two different polypeptides capable of detecting polypeptides, suchas antibodies (e.g., at least three, at least five, at least ten, atleast 20, at least 30, at least 40, at least 50, or at least 60different polypeptides capable of detecting polypeptides). The arraysprovided herein also can contain multiple copies of each of manydifferent polypeptides. In addition, the arrays for detectingpolypeptides provided herein can contain polypeptides attached to anysuitable surface (e.g., plastic or glass).

A polypeptide capable of detecting a polypeptide can be naturallyoccurring, recombinant, or synthetic. The polypeptides immobilized on anarray also can be antibodies. An antibody can be, without limitation, apolyclonal, monoclonal, human, humanized, chimeric, or single-chainantibody, or an antibody fragment having binding activity, such as a Fabfragment, F(ab′) fragment, Fd fragment, fragment produced by a Fabexpression library, fragment comprising a VL or VH domain, or epitopebinding fragment of any of the above. An antibody can be of any type,(e.g., IgG, IgM, IgD, IgA or IgY), class (e.g., IgG1, IgG4, or IgA2), orsubclass. In addition, an antibody can be from any animal includingbirds and mammals. For example, an antibody can be a mouse, chicken,human, rabbit, sheep, or goat antibody. Such an antibody can be capableof binding specifically to a polypeptide encoded by a nucleic acidlisted in Table 2 or 3. The polypeptides immobilized on the array can bemembers of a family such as a receptor family, protease family, or anenzyme family.

Antibodies can be generated and purified using any suitable methodsknown in the art. For example, monoclonal antibodies can be preparedusing hybridoma, recombinant, or phage display technology, or acombination of such techniques. In some cases, antibody fragments can beproduced synthetically or recombinantly from a nucleic acid encoding thepartial antibody sequence. In some cases, an antibody fragment can beenzymatically or chemically produced by fragmentation of an intactantibody. In addition, numerous antibodies are available commercially(Table 1). An antibody directed against a polypeptide encoded by anucleic acid listed in Table 2 or 3 can bind the polypeptide at anaffinity of at least 10⁴ mol⁻¹ (e.g., at least 10⁵, 10⁶, 10⁷, 10⁸, 10⁹,10¹⁰, 10¹¹, or 10¹² mol⁻¹).

TABLE 1 Commercially available antibodies directed against extracellularor membrane-associated polypeptides Nucleic Acid Symbol Antibody NameSupplier Catalog No. Clone APOC1 Apolipoprotein C-1 Abcam, ab20120 mouseantibody Cambridge, MA ASPN Asporin antibody Imgenex, San IMG-3803 goatDiego, CA C20orf102 C20orf102 antibody Abnova, Taipei, H00128434- clone3B9 Taiwan M01 COL2A1 COL2A1 monoclonal Abnova, Taipei, H00001280-#3H1-9 antibody Taiwan M01 HLA-DMB HLA-DMB monoclonal Abnova, Taipei,H00003109- clone 6B3 antibody Taiwan M01 MMP26 Rabbit antibody to TriplePoint RP3MMP26 rabbit MMP-26 Biologics, Forest Grove, OR NRN1 Anti-humanNeuritin R&D Systems, AF283 goat antibody Minneapolis, MN SFRP4 SFRP4polyclonal Abnova, Taipei, H00006424- mouse poly antibody Taiwan A01CHRM3 CHRM3 polyclonal Abnova, Taipei, H00001131- mouse poly antibodyTaiwan A01 OR51E2 PSGR antibody Novus, Littleton, ab13383 rabbit COTMPRSS2 TMPRSS2 (h-50) Santa Cruz sc-33533 rabbit antibodyBiotechnology, Santa Cruz, CA PLA2G7 PLA2G7 monoclonal Abnova, Taipei,H00007941- clone 5D1 antibody Taiwan M02 FZD8 FZD8 polycolonal Abnova,Taipei, H00008325- mouse poly antibody Taiwan A01 GJB1 Connexin 32/GJB1Abcam, ab11366 CXN-32 antibody [CXN-32] Cambridge, MA MSMB ProstateSecretory Abcam, ab19070 YPSP-1 Protein/PSP antibody Cambridge, MA[YPSP-1] MSMB MSMB polyclonal Abnova, Taipei, H00004477- mouse polyantibody Taiwan A01 MSMB Mab to human Prostate BIODESIGN, M14841M BDI841Secretory protein Saco, ME MSMB Mab to human Prostate BIODESIGN, M14248MBDI248 Secretory protein Saco, ME MSMB MSMB polyclonal Novus, Littleton,H00004477- mouse poly antibody CO A01 ADAMTS8 ADAMTS8 antibody Abcam,ab28597 rabbit Cambridge, MA ADAMTS8 ADAMTS8 monoclonal Abnova, Taipei,H00011095- clone 5A3 antibody Taiwan M01 ADAMTS8 Rabbit anti ADAM-Accurate, ACL2ADA rabbit TS8, amino terminal Westbury, NY MTS8 ADAMTS8Rabbit anti ADAM- Accurate, ACL1ADA rabbit TS8, carboxy terminalWestbury, NY MTS8 ALDH3B2 ALDH3B2 monoclonal Abnova, Taipei, H00000222-clone 3E6 antibody Taiwan M01 EFNA4 Ephrin A4 Antibody Novus, Littleton,ab7041 goat CO GRIN3A NMDAR3A+3B Abcam, ab2639 mouse Cambridge, MAGRIN3A NMDAR3A+3B Novus, Littleton, H00002904- mouse antibody CO A01GRIN3A NMDAR NR3A/B QED, San Diego, 60100 rabbit antibody CA HPN Hepsinantibody Abcam, ab31149 Duck/IgY Cambridge, MA HPN Hepsin antibodyAbcam, ab31148 rabbit Cambridge, MA HPN HPN monoclonal Abnova, Taipei,H00003249- clone 3E3 antibody Taiwan M01 ITGBL1 Osteoblast SpecificAbcam, ab37176 chicken/IgY Cysteine-rich Protein Cambridge, MA LOX LOXantibody Abcam, ab31238 rabbit Cambridge, MA MUC1 MUC-1 polyclonalAbnova, Taipei, H00004582- mouse poly antibody Taiwan A01 NRP1 NRP1monoclonal Abnova, Taipei, H00008829- 1B3 antibody Taiwan M05 NRP1Anti-Neuropilin-1 (CUB ECM Biosciences NP2111 rabbit Domain) NRP1Neuropilin (A-12) Santa Cruz sc-5307 mouse mono antibody Biotechnology,Santa Cruz, CA PCDHB10 PCDHB10 polyclonal Abnova, Taipei, H00056126-mouse poly antibody Taiwan A01 PCSK6 PCSK6 plyclonal Abnova, Taipei,H00005046- mouse poly antibody Taiwan A01 PSCA PSCA monoclonal Abnova,Taipei, H00008000- 5c2 antibody Taiwan M03

Any method can be used to make an array for detecting polypeptides. Forexample, methods disclosed in U.S. Pat. No. 6,630,358 can be used tomake arrays for detecting polypeptides. Arrays for detectingpolypeptides can also be obtained commercially, such as from Panomics,Redwood City, Calif.

This document also provides nucleic acid arrays. The arrays providedherein can be two-dimensional arrays, and can contain at least twodifferent nucleic acid molecules (e.g., at least three, at least five,at least ten, at least 20, at least 30, at least 40, at least 50, or atleast 60 different nucleic acid molecules). Each nucleic acid moleculecan have any length. For example, each nucleic acid molecule can bebetween 10 and 250 nucleotides (e.g., between 12 and 200, 14 and 175, 15and 150, 16 and 125, 18 and 100, 20 and 75, or and 50 nucleotides) inlength. In some cases, an array can contain one or more cDNA moleculesencoding, for example, partial or entire polypeptides. In addition, eachnucleic acid molecule can have any sequence. For example, the nucleicacid molecules of the arrays provided herein can contain sequences thatare present within the nucleic acids listed in Tables 2 and 3.

Typically, at least 25% (e.g., at least 30%, at least 40%, at least 50%,at least 60%, at least 75%, at least 80%, at least 90%, at least 95%, or100%) of the nucleic acid molecules of an array provided herein containa sequence that is (1) at least 10 nucleotides (e.g., at least 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 25, or more nucleotides) in length and(2) at least about 95 percent (e.g., at least about 96, 97, 98, 99, or100) percent identical, over that length, to a sequence present within anucleic acid listed in Table 2 or 3. For example, an array can contain60 nucleic acid molecules located in known positions, where each of the60 nucleic acid molecules is 100 nucleotides in length while containinga sequence that is (1) 30 nucleotides is length, and (2) 100 percentidentical, over that 30 nucleotide length, to a sequence of one of thenucleic acids listed in Table 2. Thus, a nucleic acid molecule of anarray provided herein can contain a sequence present within a nucleicacid listed in Table 2 or 3 where that sequence contains one or more(e.g., one, two, three, four, or more) mismatches.

The nucleic acid arrays provided herein can contain nucleic acidmolecules attached to any suitable surface (e.g., plastic or glass). Inaddition, any method can be use to make a nucleic acid array. Forexample, spotting techniques and in situ synthesis techniques can beused to make nucleic acid arrays. Further, the methods disclosed in U.S.Pat. Nos. 5,744,305 and 5,143,854 can be used to make nucleic acidarrays.

In some cases, a sample from a mammal can be assessed forauto-antibodies against a polypeptide encoded by any of the nucleic acidmolecules provided herein. The presence of such auto-antibodies canindicate that the mammal has prostate cancer. For example, a bloodsample from a human can be assessed for the presence of auto-antibodiesto a polypeptide encoded by any of the nucleic acid molecules providedherein with the presence of such an auto-antibody indicating that thathuman has prostate cancer.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Identification of Nucleic Acids EncodingExtracellular and Membrane-Associated Polypeptides that can be Used toIdentify Prostate Cancer

Gene expression was profiled in prostate epithelial cells. Benign andmalignant cells were laser capture microdissected from 100 prostatetissues and metastatic prostatic adenocarcinomas. Non-neoplasticprostate epithelial cells were collected from the tissues of 29 patientshaving prostate cancer. High-grade prostatic intraepithelial neoplasia(PIN) cells, metastatic prostate cancer cells, and primary Gleasonpattern 3, 4, and 5 cells were collected from the remaining tissues. RNAwas extracted from homogenous populations of captured cells andpurified. Samples of total RNA were linearly amplified, labeled, andhybridized to U133 Plus 2.0 arrays (Affymetrix, Santa Clara, Calif.).The arrays were washed, stained, and scanned in accordance withAffymetrix protocols.

Secreted and membrane bound polypeptides associated with the Affymetrixprobe sets were identified using two methods. First, RefSeq polypeptidesequence identifiers annotated to the probe set identifiers wereabstracted from the Affymetrix U133 Plus 2.0 annotation file. Thesesequences were downloaded from NCBI and processed through a predictionpipeline, which included SignalP analysis, TargetP analysis, TMHMManalysis, and Phobius analysis. Polypeptides predicted to be secretorypolypeptides by the SignalP and TargetP programs were further analyzedusing the TMHMM and Phobius programs. Polypeptides that were notpredicted to be secretory polypeptides by the SignalP program or theTargetP program were classified as non-secretory polypeptides. Secretorypolypeptides predicted to have no transmembrane domains by the TMHMMprogram were classified as extracellular. Secretory polypeptidespredicted to have two or more transmembrane domains were classified asmembrane-associated polypeptides. Secretory polypeptides predicted tohave only one transmembrane domain were analyzed using the Phobiusprogram. Phobius predictions were used to differentiate polypeptideswith N-terminal signal anchors (uncleaved) from polypeptides withN-terminal signal sequences (cleaved). The second method used toidentify secreted and membrane polypeptides involved mining thelocalization annotated database of SWISS-PROT polypeptides. TheSwissProt records for all human polypeptides were downloaded. Alllocalization annotations were manually reviewed and categorized asextracellular (S), plasma membrane (M), or intracellular (I). All probesets with annotated SwissProt polypeptides having cellular localizationannotations were classified extracellular (S), plasma membrane (M), orintracellular (I). Localization classifications assigned by SwissProtannotations were given preference over classifications made by theprediction analyses. A set of 70 nucleic acids encoding extracellularand membrane-associated polypeptides was identified, including 53nucleic acids that were annotated or predicted to encode extracellularpolypeptides, and 17 nucleic acids that were annotated or predicted toencode membrane-associated polypeptides.

The value of the selected nucleic acids for use in identifying cancerwas assessed using two methods. Fifty-four polypeptides, including allof the membrane-associated polypeptides, were selected based onup-regulation of corresponding RNA transcripts observed in prostatecancer cells as compared to non-neoplastic prostate cells. The initiallist of differentially expressed nucleic acids was identified usingseveral microarray analysis parameters, including:

a. PM/MM normalization and no transformation

b. PM only normalization and no transformation

c. PM/MM normalization and log2 transformation

d. PM only normalization and log2 transformation Expression valuesgenerated from these analysis methods were then used to make thefollowing comparisons:

a. Gleason pattern 3 versus

-   -   Non-neoplastic (excluding Benign Prostatic Hyperplasia (BPH))

b. Gleason pattern 3 versus

-   -   Non-neoplastic+BPH

c. Gleason pattern 3+Gleason pattern 4 versus

-   -   Non-neoplastic (excluding BPH)

d. Gleason pattern 3+Gleason pattern 4 versus

-   -   Non-neoplastic+BPH

e. All Cancer versus

-   -   Non-neoplastic (excluding BPH)

f. All Cancer versus

-   -   Non-neoplastic+BPH

Nucleic acids demonstrating at least two fold up-regulation in cancercells compared to non-neoplastic cells were cross-referenced withnucleic acids classified as encoding either secretory ormembrane-associated polypeptides. The resulting list of nucleic acidswas manually curated to remove cases with expression levels below thenoise level of the microarray experiment, and cases having an expressionprofile that was over-biased by one or two aberrant cases.

The remaining sixteen nucleic acids were selected because they had ahigh level of expression in prostate cells and a prostate-preferentialexpression profile, without clear differential expression between cancerand non-cancer cells. Tissue specificity was quantitated by miningExpressed Sequence Tag transcripts.

The 70 nucleic acids selected were cross-referenced with the CancerGenome Anatomy Project's SAGE Genie, the Ludwig Institute for CancerResearch MPSS database, the Human Protein Atlas database, and an ESTtissue specificity analysis database. Based on these additionaltranscriptomic and immunohistochemistry annotations, the nucleic acidswere prioritized with numeric rankings from 1 (highest priority) tothree (lowest priority). The selected nucleic acids are listed in Tables2-4.

TABLE 2 Nucleic acids encoding extracellular or membrane-associatedpolypeptides that can be used to identify prostate cancer. Nucleic AcidRefSeq Protein Symbol Selection Process Identifier Category LocalizationAPOC1 Increased expression NP_001636.1 1 Extracellular in cancer cellsversus non-cancer cells ASPN Increased expression NP_060150.3 1Extracellular in cancer cells versus non-cancer cells BCMP11 Increasedexpression NP_789783.1 1 Extracellular in cancer cells versus non-cancercells C20orf102 Increased expression NP_542174.1 1 Extracellular incancer cells versus non-cancer cells COL2A1 Increased expressionNP_001835.2 1 Extracellular in cancer cells versus NP_149162.1non-cancer cells F5 Increased expression NP_000121.1 1 Extracellular incancer cells versus non-cancer cells HLA-DMB Increased expressionNP_002109.1 1 Extracellular in cancer cells versus non-cancer cellsLRRN1 Increased expression NP_065924.2 1 Extracellular in cancer cellsversus non-cancer cells MMP26 Increased expression NP_068573.2 1Extracellular in cancer cells versus non-cancer cells NRN1 Increasedexpression NP_057672.1 1 Extracellular in cancer cells versus non-cancercells OGDHL Increased expression NP_060715.1 1 Extracellular in cancercells versus non-cancer cells PLA1A Increased expression NP_056984.1 1Extracellular in cancer cells versus non-cancer cells PLA2G7 Increasedexpression NP_005075.2 1 Extracellular in cancer cells versus non-cancercells SFRP4 Increased expression NP_003005.1 1 Extracellular in cancercells versus non-cancer cells ALDH3B2 Increased expression NP_000686.2 2Extracellular in cancer cells versus NP_001026786.1 non-cancer cellsAPOF Increased expression NP_001629.1 2 Extracellular in cancer cellsversus non-cancer cells B3Gn-T6 Increased expression NP_619651.2 2Extracellular in cancer cells versus non-cancer cells C4A /// C4BIncreased expression NP_001002029.1 2 Extracellular in cancer cellsversus NP_009224.2 non-cancer cells COL9A2 Increased expressionNP_001843.1 2 Extracellular in cancer cells versus non-cancer cells COMPIncreased expression NP_000086.2 2 Extracellular in cancer cells versusnon-cancer cells CXCL11 Increased expression NP_005400.1 2 Extracellularin cancer cells versus non-cancer cells CXCL14 Increased expressionNP_004878.2 2 Extracellular in cancer cells versus non-cancer cellsCXCL9 Increased expression NP_002407.1 2 Extracellular in cancer cellsversus non-cancer cells DHRS8 Increased expression NP_057329.1 2Extracellular in cancer cells versus non-cancer cells ITGBL1 Increasedexpression NP_004782.1 2 Extracellular in cancer cells versus non-cancercells LOX Increased expression NP_002308.2 2 Extracellular in cancercells versus non-cancer cells MUC1 Increased expression NP_001018016.1 2Extracellular in cancer cells versus NP_001018017.1 non-cancer cellsNP_001018021.1 NP_002447.4 OR51E1 Increased expression NP_689643.1 2Extracellular in cancer cells versus non-cancer cells PCSK6 Increasedexpression NP_002561.1 2 Extracellular in cancer cells versusNP_612192.1 non-cancer cells NP_612193.1 NP_612194.1 NP_612195.1NP_612196.1 NP_612197.1 NP_612198.2 RPL22L1 Increased expressionXP_498952.2 2 Extracellular in cancer cells versus XP_940025.1non-cancer cells XP_947405.1 XP_950994.1 C1orf64 Increased expressionNP_849162.1 3 Extracellular in cancer cells versus non-cancer cellsCCL19 Increased expression NP_006265.1 3 Extracellular in cancer cellsversus non-cancer cells NRP1 Increased expression NP_001019799.1 3Extracellular in cancer cells versus NP_001019800.1 non-cancer cellsNP_003864.3 SFTPA2 Increased expression NP_008857.1 3 Extracellular incancer cells versus non-cancer cells CDH10 Increased expressionNP_006718.2 1 Membrane- in cancer cells versus associated non-cancercells CDH7 Increased expression NP_004352.2 1 Membrane- in cancer cellsversus NP_387450.1 associated non-cancer cells CHRM3 Increasedexpression NP_000731.1 1 Membrane- in cancer cells versus associatednon-cancer cells FZD8 Increased expression NP_114072.1 1 Membrane- incancer cells versus associated non-cancer cells GJB1 Increasedexpression NP_000157.1 1 Membrane- in cancer cells versus associatednon-cancer cells MS4A8B Increased expression NP_113645.1 1 Membrane- incancer cells versus associated non-cancer cells OR51E2 Increasedexpression NP_110401.1 1 Membrane- in cancer cells versus associatednon-cancer cells SLC43A1 Increased expression NP_003618.1 1 Membrane- incancer cells versus associated non-cancer cells TMEM45B Increasedexpression NP_620143.1 1 Membrane- in cancer cells versus associatednon-cancer cells FAM77C Increased expression NP_078798.1 2 Membrane- incancer cells versus associated non-cancer cells GPR116 Increasedexpression NP_056049.3 2 Membrane- in cancer cells versus associatednon-cancer cells GRIN3A Increased expression NP_597702.1 2 Membrane- incancer cells versus associated non-cancer cells HPN Increased expressionNP_002142.1 2 Membrane- in cancer cells versus NP_892028.1 associatednon-cancer cells PCDHB10 Increased expression NP_061753.1 2 Membrane- incancer cells versus associated non-cancer cells PCDHGA4 Increasedexpression NP_061740.1 2 Membrane- in cancer cells versus NP_114442.1associated non-cancer cells PRG-3 Increased expression NP_060223.2 2Membrane- in cancer cells versus NP_997182.1 associated non-cancer cellsRET Increased expression NP_065681.1 2 Membrane- in cancer cells versusNP_066124.1 associated non-cancer cells ACPP High-level, prostate-NP_001090.2 1 Extracellular preferential expression FAM61B High-level,prostate- NP_653304.1 1 Extracellular preferential expression MSMBHigh-level, prostate- NP_002434.1 1 Extracellular preferentialexpression NP_619540.1 PGLS High-level, prostate- NP_036220.1 1Extracellular preferential expression RBM35A High-level, prostate-NP_001030087.1 1 Extracellular preferential expression NP_060167.2TMPRSS2 High-level, prostate- NP_005647.2 1 Extracellular preferentialexpression LOC284591 High-level, prostate- XP_932207.1 2 Extracellularpreferential expression XP_941863.1 ADAMTS8 High-level, prostate-NP_008968.3 2 Extracellular preferential expression EFNA4 High-level,prostate- NP_005218.1 3 Extracellular preferential expressionNP_872631.1 NP_872632.1 KAZALD1 High-level, prostate- NP_112191.2 3Extracellular preferential expression SEMA3F High-level, prostate-NP_004177.2 3 Extracellular preferential expression UCN High-level,prostate- NP_003344.1 3 Extracellular preferential expression PRAC2High-level, prostate- Entrez Gene 3 Extracellular preferentialexpression 360205

TABLE 3 Nucleic acids encoding extracellular polypeptides that can beused in combination with one or more polypeptides encoded by nucleicacids listed in Table 2 to identify prostate cancer. Nucleic Acid RefSeqProtein Symbol Selection Process Identifier Category Localization CRISP3Increased expression NP_006052.1 1 Extracellular in cancer cells versusnon-cancer cells AMACR Increased expression NP_055139.4 3 Extracellularin cancer cells versus NP_976316.1 non-cancer cells KLK2 High-level,prostate- NP_001002231.1 1 Extracellular preferential expressionNP_001002232.1 NP_005542.1 KLK3 High-level, prostate- NP_001025218.1 1Extracellular preferential expression NP_001025219.1 NP_001025220.1NP_001025221.1 NP_001639.1 KLK4 High-level, prostate- NP_004908.2 2Extracellular preferential expression PSCA High-level, prostate-NP_005663.1 2 Extracellular preferential expression

TABLE 4 Nucleic acids encoding extracellular or membrane-associatedpolypeptides that are differentially expressed in cancerous andnon-cancerous prostate epithelial cells. Nucleic Acid RefSeq ProteinSymbol Selection Process Identifier Category Localization APOC1Increased expression NP_001636.1 1 Extracellular in cancer cells versusnon-cancer cells ASPN Increased expression NP_060150.3 1 Extracellularin cancer cells versus non-cancer cells BCMP11 Increased expressionNP_789783.1 1 Extracellular in cancer cells versus non-cancer cellsC20orf102 Increased expression NP_542174.1 1 Extracellular in cancercells versus non-cancer cells COL2A1 Increased expression NP_001835.2 1Extracellular in cancer cells versus NP_149162.1 non-cancer cells F5Increased expression NP_000121.1 1 Extracellular in cancer cells versusnon-cancer cells HLA-DMB Increased expression NP_002109.1 1Extracellular in cancer cells versus non-cancer cells LRRN1 Increasedexpression NP_065924.2 1 Extracellular in cancer cells versus non-cancercells MMP26 Increased expression NP_068573.2 1 Extracellular in cancercells versus non-cancer cells NRN1 Increased expression NP_057672.1 1Extracellular in cancer cells versus non-cancer cells OGDHL Increasedexpression NP_060715.1 1 Extracellular in cancer cells versus non-cancercells PLA1A Increased expression NP_056984.1 1 Extracellular in cancercells versus non-cancer cells PLA2G7 Increased expression NP_005075.2 1Extracellular in cancer cells versus non-cancer cells SFRP4 Increasedexpression NP_003005.1 1 Extracellular in cancer cells versus non-cancercells ALDH3B2 Increased expression NP_000686.2 2 Extracellular in cancercells versus NP_001026786.1 non-cancer cells APOF Increased expressionNP_001629.1 2 Extracellular in cancer cells versus non-cancer cellsB3Gn-T6 Increased expression NP_619651.2 2 Extracellular in cancer cellsversus non-cancer cells C4A /// C4B Increased expression NP_001002029.12 Extracellular in cancer cells versus NP_009224.2 non-cancer cellsCOL9A2 Increased expression NP_001843.1 2 Extracellular in cancer cellsversus non-cancer cells COMP Increased expression NP_000086.2 2Extracellular in cancer cells versus non-cancer cells CXCL11 Increasedexpression NP_005400.1 2 Extracellular in cancer cells versus non-cancercells CXCL14 Increased expression NP_004878.2 2 Extracellular in cancercells versus non-cancer cells CXCL9 Increased expression NP_002407.1 2Extracellular in cancer cells versus non-cancer cells DHRS8 Increasedexpression NP_057329.1 2 Extracellular in cancer cells versus non-cancercells ITGBL1 Increased expression NP_004782.1 2 Extracellular in cancercells versus non-cancer cells LOX Increased expression NP_002308.2 2Extracellular in cancer cells versus non-cancer cells MUC1 Increasedexpression NP_001018016.1 2 Extracellular in cancer cells versusNP_001018017.1 non-cancer cells NP_001018021.1 NP_002447.4 OR51E1Increased expression NP_689643.1 2 Extracellular in cancer cells versusnon-cancer cells PCSK6 Increased expression NP_002561.1 2 Extracellularin cancer cells versus NP_612192.1 non-cancer cells NP_612193.1NP_612194.1 NP_612195.1 NP_612196.1 NP_612197.1 NP_612198.2 RPL22L1Increased expression XP_498952.2 2 Extracellular in cancer cells versusXP_940025.1 non-cancer cells XP_947405.1 XP_950994.1 C1orf64 Increasedexpression NP_849162.1 3 Extracellular in cancer cells versus non-cancercells CCL19 Increased expression NP_006265.1 3 Extracellular in cancercells versus non-cancer cells NRP1 Increased expression NP_001019799.1 3Extracellular in cancer cells versus NP_001019800.1 non-cancer cellsNP_003864.3 SFTPA2 Increased expression NP_008857.1 3 Extracellular incancer cells versus non-cancer cells CDH10 Increased expressionNP_006718.2 1 Membrane- in cancer cells versus associated non-cancercells CDH7 Increased expression NP_004352.2 1 Membrane- in cancer cellsversus NP_387450.1 associated non-cancer cells CHRM3 Increasedexpression NP_000731.1 1 Membrane- in cancer cells versus associatednon-cancer cells FZD8 Increased expression NP_114072.1 1 Membrane- incancer cells versus associated non-cancer cells GJB1 Increasedexpression NP_000157.1 1 Membrane- in cancer cells versus associatednon-cancer cells MS4A8B Increased expression NP_113645.1 1 Membrane- incancer cells versus associated non-cancer cells OR51E2 Increasedexpression NP_110401.1 1 Membrane- in cancer cells versus associatednon-cancer cells SLC43A1 Increased expression NP_003618.1 1 Membrane- incancer cells versus associated non-cancer cells TMEM45B Increasedexpression NP_620143.1 1 Membrane- in cancer cells versus associatednon-cancer cells FAM77C Increased expression NP_078798.1 2 Membrane- incancer cells versus associated non-cancer cells GPR116 Increasedexpression NP_056049.3 2 Membrane- in cancer cells versus associatednon-cancer cells GRIN3A Increased expression NP_597702.1 2 Membrane- incancer cells versus associated non-cancer cells HPN Increased expressionNP_002142.1 2 Membrane- in cancer cells versus NP_892028.1 associatednon-cancer cells PCDHB10 Increased expression NP_061753.1 2 Membrane- incancer cells versus associated non-cancer cells PCDHGA4 Increasedexpression NP_061740.1 2 Membrane- in cancer cells versus NP_114442.1associated non-cancer cells PRG-3 Increased expression NP_060223.2 2Membrane- in cancer cells versus NP_997182.1 associated non-cancer cellsRET Increased expression NP_065681.1 2 Membrane- in cancer cells versusNP_066124.1 associated non-cancer cells

Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

1. An enzyme-linked immunosorbent assay method for identifying a malehuman as having prostate cancer, said method comprising: (a) obtaining aserum sample of a male human, (b) performing an enzyme-linkedimmunosorbent assay to detect the presence of an elevated level of apolypeptide encoded by an ASPN, PCSK6, RPL22L1, or CDH7 nucleic acidwithin said sample, and (c) classifying said male human as havingprostate cancer based at least in part on said presence.
 2. The methodof claim 1, wherein said polypeptide is a polypeptide encoded by saidASPN nucleic acid.
 3. The method of claim 1, wherein said polypeptide isa polypeptide encoded by said PCSK6 nucleic acid.
 4. The method of claim1, wherein said polypeptide is a polypeptide encoded by said RPL22L1nucleic acid.
 5. The method of claim 1, wherein said polypeptide is apolypeptide encoded by said CDH7 nucleic acid.